Hi, I am new here.
What I think about qiime2 is that I can do further analysis with asv or otu. So I will do both and choose one that gives best result for my project.
For asv, we do [cutadapt - dada2] and get [FeatureTable], [FeatureData] as an output.
For otu, we do [cutadapt - joinpairs(vsearch) - qualityfilter - dereplicate(vsearch)] and get [FeatureTable], [FeatureData].
So questions I have is
For the asv, in the dada2, there are options like trim and trunc. So if I do dada2, do I need to run cutadapt? or should I just pass cutadapt?
For the otu clustering, I think I should get rid of adaptor sequences(right?). And those are the adaptor seqs I got.
mlCOIintF: 5’-GGWACWGGWTGAACWGTWTAYCCYCC-3’, jgHCO2198: 5’-TAIACYTCIGGRTGICCRAARAAYCA-3’
(W: A or T, R: A or G, Y: C or T)
So I run cutadapt as below
$qiime cutadapt trim-paired --i-demultiplexed-sequences demux.qza --p-adapter-f ‘GGWACWGGWTGAACWGTWTAYCCYCC’ --p-adapter-r ‘TAIACYTCIGGRTGICCRAARAAYCA’ --p-error-rate 0.1 --o-trimmed-sequences cutadapt-demux.qza --verbose
and got this error.
cutadapt: error: Character ‘I’ in adapter sequence ‘TAIACYTCIGGRTGICCRAARAAYCA^’ is not a valid IUPAC code. Use only characters XACGTURYSWKMBDHVN.
Traceback (most recent call last):
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in trim_paired
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/site-packages/q2_cutadapt/_trim.py”, line 189, in trim_paired
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/site-packages/q2_cutadapt/_trim.py”, line 30, in run_commands
File “/home/creo9447/miniconda3/envs/qiime/lib/python3.6/subprocess.py”, line 438, in run
I really need some help.